It might just be me, but I'd be nervous about the open holes too. Measure them and poke around online for matching plugs. These are common items in many vehicles from all the American car manufacturers, and I've found them at auto swap meets. Use a search engine with the term "automotive door plug", "panel plug", etc. They come in different sizes, inch and metric.
Allegedly modern vehicles are rustproofed at the factory, but while the holes are open, you might want to consider getting the inside of those panels treated. When I was looking at old Rangers, I found that Ford merely painted the frame, and Rangers from up north would have serious frame rust from road salt. Certain years, especially 1998–2005, are notorious for frame failure from rust-through.
Just because you have a new Ranger doesn't mean it might not be a problem one day. I still see surprisingly recent full-sized trucks with rusted-out rocker panels, including Fords.
The 2011 Ranger I recently bought had been fully treated, including the bed sprayed with Line-X. It had also been a southeastern Virginia truck its whole life, which helped with lack of salt exposure. That was the deciding factor in my buying the truck.
Hope this helps.